Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5′ to 3′ degradation

Abstract

Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling. Here, we use a non-invasive method for estimating half-lives for hundreds of mRNAs in the early Drosophila embryo. This approach uses the intronic and exonic reads from a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs. We show how regulation of mRNA stability is used to establish a range of mature mRNA dynamics during embryogenesis, despite shared transcription profiles. Using single-molecule imaging, we provide evidence that, for the mRNAs tested, there is a correlation between short half-life and mRNA association with P-bodies. Moreover, we detect an enrichment of mRNA 3′ ends in P-bodies in the early embryo, consistent with 5′ to 3′ degradation occurring in P-bodies for at least a subset of mRNAs. We discuss our findings in relation to recently published data suggesting that the primary function of P-bodies in other biological contexts is mRNA storage.

A spatiotemporally resolved atlas of mRNA decay in theC. elegansembryo reveals differential regulation of mRNA stability across stages and cell types

“…Previous studies in cell culture systems found that median half-life is roughly proportional to cell cycle length (Vejnar et al 2019). A study of decay in early Drosophila melanogaster embryos (nc11 through cephalic furrow formation), which have comparable cell cycle lengths (~10-180 minutes) to those in the C. elegans embryo (Foe 1989;Bao et al 2008), observed a similar range of half-lives to ours for ~260 zygotic transcripts (Beadle et al 2023). In older fly embryos (stage 12 to 15), which have longer cell cycles, the median half-life was longer at 73 minutes (Burow et al 2015).…”

Multiplexed Assays of Human Disease-relevant Mutations Reveal UTR Dinucleotide Composition as a Major Determinant of RNA Stability

“…As another layer of validation, we further explored their relative contributions to mRNA enrichment in P-bodies (Courel et al, 2019). P-bodies are membraneless granules for RNA storage and turnover (Beadle et al, 2023). We uncovered a positive correlation between TA dinucleotides and RNA P-body localization, especially for those occurring in 3’ UTRs (Fig.…”

Relating the Biogenesis and Function of P Bodies in Drosophila to Human Disease

“…Later, in early embryogenesis, smaller and more dynamic P bodies reform [ 38 ], and this offers a unique avenue for the study of de novo condensate formation. Current work shows degradation intermediates for short-lived mRNAs accumulating in reformed P bodies during embryogenesis [ 54 ], and P body components Me31B, Decapping protein 1 (DCP1), Staufen (Stau), and Pacman (Pcm) accumulate with oskar ( osk ) mRNA, and this correlates with the degradation of the mRNA [ 55 ]. Additionally, biochemical data suggest that Me31B transitions from a translational repressor to a beacon for mRNA degradation after the maternal to zygotic transition (MZT) [ 56 ].…”

“…Unfortunately, there are only a few well-documented examples of RNAs that associate with P bodies in Drosophila [ 42 , 54 , 95 ], and more research is needed to fully understand the importance of RNA in P body biogenesis.…”

“…By creating multiple short nucleotide oligomer probes conjugated to a fluorophore [ 131 ], it is possible to label RNA with great specificity and a minimal background. In combination with super-resolution imaging, this method can visualise the sub-granule localisation of single mRNA molecules [ 38 , 54 , 101 , 102 , 103 , 104 , 105 , 106 ].…”